Variant report

Variant	rs4840581
Chromosome Location	chr8:11635569-11635570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr8:11635564-11636210	SK-N-SH	brain:	n/a	chr8:11635873-11635894 chr8:11635878-11635887 chr8:11635852-11635861 chr8:11635878-11635887
2	ESR1	chr8:11635435-11635694	T-47D	breast:	n/a	chr8:11635640-11635657

No.	Distal block	Cell Line	Cell type
1	chr8:11635165..11636835-chr8:11660450..11662194,2	MCF-7	breast:
2	chr8:11635229..11636009-chr8:11646882..11647706,2	MCF-7	breast:
3	chr8:11587913..11588513-chr8:11635440..11636177,3	MCF-7	breast:
4	chr8:11587913..11588721-chr8:11635440..11636177,4	MCF-7	breast:
5	chr8:11635191..11637008-chr8:11641548..11643752,2	K562	blood:
6	chr8:11629548..11632235-chr8:11633790..11635730,3	MCF-7	breast:

Variant related genes	Relation type
NEIL2	TF binding region
ENSG00000079459	Chromatin interaction
ENSG00000227203	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004712	0.88[CEU][hapmap]
rs10098874	1.00[JPT][hapmap]
rs1047643	1.00[JPT][hapmap]
rs1090107	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1122182	1.00[CHB][hapmap]
rs11777273	1.00[CHB][hapmap]
rs1293292	1.00[CHB][hapmap]
rs1293294	1.00[CHB][hapmap]
rs1293297	1.00[CHB][hapmap]
rs1293298	1.00[CHB][hapmap]
rs1293300	1.00[CHB][hapmap]
rs1466785	0.84[CEU][hapmap]
rs1692811	1.00[CHB][hapmap]
rs1692821	1.00[CHB][hapmap]
rs1736081	1.00[CHB][hapmap]
rs1736086	1.00[CHB][hapmap]
rs17754589	1.00[JPT][hapmap]
rs2686187	0.96[CEU][hapmap]
rs2740435	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2740592	1.00[CHB][hapmap]
rs3947	1.00[CHB][hapmap]
rs4639	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs4839	1.00[CHB][hapmap]
rs4841567	1.00[CHB][hapmap]
rs709821	1.00[CHB][hapmap]
rs709822	1.00[CHB][hapmap]
rs7831946	1.00[CHB][hapmap]
rs804258	0.84[CEU][hapmap]
rs804261	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs804263	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs804265	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs804266	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs804267	1.00[JPT][hapmap]
rs804269	1.00[JPT][hapmap]
rs804270	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs804271	0.80[EUR][1000 genomes]
rs804276	0.83[CEU][hapmap]
rs8191604	1.00[JPT][hapmap]
rs8191649	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4840581	FCRL4	trans	lymphoblastoid	RTeQTL
rs4840581	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs4840581	NEIL2	cis	Nerve Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11628000-11640800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:11628400-11635800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr8:11628400-11637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:11628400-11640000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr8:11628400-11640600	Weak transcription	A549	lung
6	chr8:11628400-11640600	Weak transcription	NH-A	brain
7	chr8:11628400-11641200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:11628400-11641200	Weak transcription	Psoas Muscle	Psoas
9	chr8:11628400-11641400	Weak transcription	Esophagus	oesophagus
10	chr8:11628400-11647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr8:11628400-11653000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr8:11628400-11656800	Weak transcription	Small Intestine	intestine
13	chr8:11628600-11636800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr8:11628600-11637200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:11628600-11638000	Weak transcription	NHEK	skin
16	chr8:11628600-11638400	Weak transcription	NHLF	lung
17	chr8:11628600-11638800	Weak transcription	HMEC	breast
18	chr8:11628600-11640600	Weak transcription	Osteobl	bone
19	chr8:11628600-11640800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:11628600-11641800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr8:11628600-11647200	Weak transcription	Fetal Heart	heart
22	chr8:11628800-11638200	Weak transcription	NHDF-Ad	bronchial
23	chr8:11628800-11639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr8:11628800-11640200	Weak transcription	Pancreas	Pancrea
25	chr8:11628800-11640400	Weak transcription	HSMMtube	muscle
26	chr8:11628800-11640600	Weak transcription	Placenta	Placenta
27	chr8:11628800-11640600	Weak transcription	HepG2	liver
28	chr8:11628800-11640800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:11628800-11640800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr8:11628800-11641000	Weak transcription	Colon Smooth Muscle	Colon
31	chr8:11628800-11641200	Weak transcription	HSMM	muscle
32	chr8:11628800-11641600	Weak transcription	Colonic Mucosa	Colon
33	chr8:11628800-11646800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr8:11629000-11638000	Weak transcription	Brain Germinal Matrix	brain
35	chr8:11629000-11640200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr8:11629000-11640400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:11629000-11640800	Weak transcription	Gastric	stomach
38	chr8:11629000-11640800	Weak transcription	Right Ventricle	heart
39	chr8:11629000-11641000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr8:11629000-11641600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr8:11629200-11636000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr8:11629200-11637200	Weak transcription	Lung	lung
43	chr8:11629200-11640200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr8:11629200-11640800	Weak transcription	Fetal Intestine Large	intestine
45	chr8:11629200-11644200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr8:11629400-11638800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr8:11629400-11640000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr8:11629400-11640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr8:11629400-11640400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr8:11629600-11638400	Strong transcription	Fetal Muscle Leg	muscle

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